Increased lipid production by heterologous expression of AtWRI1 transcription factor in Nannochloropsis salina

Harnessing genetic engineering to drive economic bioproduct production in algae

Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.

Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities

The development of microalgal biofuels is of significant importance in advancing the energy transition, alleviating food pressure, preserving the natural environment, and addressing climate change. Numerous countries and regions across the globe have conducted extensive research and strategic planning on microalgal bioenergy, investing significant funds and manpower into this field. However, the microalgae biofuel industry has faced a downturn due to the constraints of high costs. In the past decade, with the development of new strains, technologies, and equipment, the feasibility of large-scale production of microalgae biofuel should be re-evaluated. Here, we have gathered research results from the past decade regarding microalgae biofuel production, providing insights into the opportunities and challenges faced by this industry from the perspectives of microalgae selection, modification, and cultivation. In this review, we suggest that highly adaptable microalgae are the preferred choice for large-scale biofuel production, especially strains that can utilize high concentrations of inorganic carbon sources and possess stress resistance. The use of omics technologies and genetic editing has greatly enhanced lipid accumulation in microalgae. However, the associated risks have constrained the feasibility of large-scale outdoor cultivation. Therefore, the relatively controllable cultivation method of photobioreactors (PBRs) has made it the mainstream approach for microalgae biofuel production. Moreover, adjusting the performance and parameters of PBRs can also enhance lipid accumulation in microalgae. In the future, given the relentless escalation in demand for sustainable energy sources, microalgae biofuels should be deemed a pivotal constituent of national energy planning, particularly in the case of China. The advancement of synthetic biology helps reduce the risks associated with genetically modified (GM) microalgae and enhances the economic viability of their biofuel production.

Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion

Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

A cheap two-step cultivation of Phaeodactylum tricornutum for increased TAG production and differential expression of TAG biosynthesis associated genes

A cheap cultivation of microalgae greatly reduces the biodiesel production cost. Subsequently in this study, citric acid and effluents from sugar and tannery industries were used as the nutritional supplements for the improvement of biomass and TAG production in Phaeodactylum tricornutum using two-step cultivation. When compared to control (media without supplementation), a considerable increase in biomass and chlorophyll a was obtained with citric acid (CA) and sugar industry effluent (SIE) supplemented media. In the two-step cultivation method, biomass raised from CA (100mg·L^-1) and SIE (1.5mL·L^-1) supplementations in the first step, viz. biomass production (BP) step was allowed for lipid accumulation in the second step, viz. lipid production (LP) step, and thus yielded enhanced lipids of 11.5 ± 0.7mg·L^-1·day^-1 and 13.5 ± 1.9mg·L^-1·day^-1 respectively, with improved TAG synthesis. Further, differential expression analysis of TAG biosynthetic genes of P. tricornutum under single-step and two-step cultivation modes were performed, and the gene expression patterns were studied.

Overexpression of Soybean GmWRI1a Stably Increases the Seed Oil Content in Soybean

WRINKLED1 (WRI1), an APETALA2/ethylene-responsive-element-binding protein (AP2/EREBP) subfamily transcription factor, plays a crucial role in the transcriptional regulation of plant fatty acid biosynthesis. In this study, GmWRI1a was overexpressed in the soybean cultivar 'Dongnong 50' using Agrobacterium-mediated transformation to generate three transgenic lines with high seed oil contents. PCR and Southern blotting analysis showed that the T-DNA was inserted into the genome at precise insertion sites and was stably inherited by the progeny. Expression analysis using qRT-PCR and Western blotting indicated that GmWRI1a and bar driven by the CaMV 35S promoter were significantly upregulated in the transgenic plants at different developmental stages. Transcriptome sequencing results showed there were obvious differences in gene expression between transgenic line and transgenic receptor during seed developmental stages. KEGG analysis found that the differentially expressed genes mainly annotated to metabolic pathways, such as carbohydrated metabolism and lipid metabolism. A 2-year single-location field trial revealed that three transgenic lines overexpressing GmWRI1a (GmWRI1a-OE) showed a stable increase in seed oil content of 4.97-10.35%. Importantly, no significant effect on protein content and yield was observed. Overexpression of GmWRI1a changed the fatty acid composition by increasing the linoleic acid (C18:2) content and decreasing the palmitic acid (C16:0) content in the seed. The three GmWRI1a-OE lines showed no significant changes in agronomic traits. The results demonstrated that the three GmWRI1a overexpression lines exhibited consistent increases in seed oil content compared with that of the wild type and did not significantly affect the seed yield and agronomic traits. The genetic engineering of GmWRI1a will be an effective strategy for the improvement of seed oil content and value in soybean.

Multi-omics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae

Microalgae, a group of photosynthetic microorganisms rich in diverse and novel bioactive metabolites, have been explored for the production of biofuels, high value-added compounds as food and feeds, and pharmaceutical chemicals as agents with therapeutic benefits. This article reviews the development of omics resources and genetic engineering techniques including gene transformation methodologies, mutagenesis, and genome-editing tools in microalgae biorefinery and wastewater treatment. The introduction of these enlisted techniques has simplified the understanding of complex metabolic pathways undergoing microalgal cells. The multiomics approach of the integrated omics datasets, big data analysis, and machine learning for the discovery of objective traits and genes responsible for metabolic pathways was reviewed. Recent advances and limitations of multiomics analysis and genetic bioengineering technology to facilitate the improvement of microalgae as the dual role of wastewater treatment and biorefinery feedstock production are discussed. This article is protected by copyright. All rights reserved.

Exploring a blue-light-sensing transcription factor to double the peak productivity of oil in Nannochloropsis oceanica

Oleaginous microalgae can produce triacylglycerol (TAG) under stress, yet the underlying mechanism remains largely unknown. Here, we show that, in Nannochloropsis oceanica, a bZIP-family regulator NobZIP77 represses the transcription of a type-2 diacylgycerol acyltransferase encoding gene NoDGAT2B under nitrogen-repletion (N+), while nitrogen-depletion (N−) relieves such inhibition and activates NoDGAT2B expression and synthesis of TAG preferably from C16:1. Intriguingly, NobZIP77 is a sensor of blue light (BL), which reduces binding of NobZIP77 to the NoDGAT2B-promoter, unleashes NoDGAT2B and elevates TAG under N−. Under N+ and white light, NobZIP77 knockout fully preserves cell growth rate and nearly triples TAG productivity. Moreover, exposing the NobZIP77-knockout line to BL under N− can double the peak productivity of TAG. These results underscore the potential of coupling light quality to oil synthesis in feedstock or bioprocess development.

Microalgae are promising feedstock for oil production. The authors report that a transcription factor NobZIP77 can regulate oil synthesis by sensing the blue light, and explore these findings to greatly enhance oil productivity via genetic and process engineering in Nannochloropsis oceanica.

Microalgal metabolic engineering strategies for the production of fuels and chemicals

Microalgae are promising sustainable resources because of their ability to convert CO₂ into biofuels and chemicals directly. However, the industrial production and economic feasibility of microalgal bioproducts are still limited. As such, metabolic engineering approaches have been undertaken to enhance the productivities of microalgal bioproducts. In the last decade, impressive advances in microalgae metabolic engineering have been made by developing genetic engineering tools and multi-omics analysis. This review presents comprehensive microalgal metabolic pathways and metabolic engineering strategies for producing lipids, long chain-polyunsaturated fatty acids, terpenoids, and carotenoids. Additionally, promising metabolic engineering approaches specific to target products are summarized. Finally, this review discusses current challenges and provides future perspectives for the effective production of chemicals and fuels via microalgal metabolic engineering.

Phyllosilicate derived catalysts for efficient conversion of lignocellulosic derived biomass to biodiesel: A review

The efforts have been made to review phyllosilicate derived (clay-based) heterogeneous catalysts for biodiesel production via lignocellulose derived feedstocks. These catalysts have many practical and potential applications in green catalysis. Phyllosilicate derived heterogeneous catalysts (modified via any of these approaches like acid activated clays, ion exchanged clays and layered double hydroxides) exhibits excellent catalytic activity for producing cost effective and high yield biodiesel. The combination of different protocols (intercalated catalysts, ion exchanged catalysts, acidic activated clay catalysts, clay-supported catalysts, composites and hybrids, pillared interlayer clay catalysts, and hierarchically structured catalysts) was implemented so as to achieve the synergetic effects (acidic-basic) in resultant material (catalyst) for efficient conversion of lignocellulose derived feedstock (non-edible oils) to biodiesel. Utilisation of these Phyllosilicate derived catalysts will pave path for future researchers to investigate the cost-effective, accessible and improved approaches in synthesising novel catalysts that could be used for converting lignocellulosic biomass to eco-friendly biodiesel.

Highly Valuable Polyunsaturated Fatty Acids from Microalgae: Strategies to Improve Their Yields and Their Potential Exploitation in Aquaculture

Microalgae have a great potential for the production of healthy food and feed supplements. Their ability to convert carbon into high-value compounds and to be cultured in large scale without interfering with crop cultivation makes these photosynthetic microorganisms promising for the sustainable production of lipids. In particular, microalgae represent an alternative source of polyunsaturated fatty acids (PUFAs), whose consumption is related to various health benefits for humans and animals. In recent years, several strategies to improve PUFAs' production in microalgae have been investigated. Such strategies include selecting the best performing species and strains and the optimization of culturing conditions, with special emphasis on the different cultivation systems and the effect of different abiotic factors on PUFAs' accumulation in microalgae. Moreover, developments and results obtained through the most modern genetic and metabolic engineering techniques are described, focusing on the strategies that lead to an increased lipid production or an altered PUFAs' profile. Additionally, we provide an overview of biotechnological applications of PUFAs derived from microalgae as safe and sustainable organisms, such as aquafeed and food ingredients, and of the main techniques (and their related issues) for PUFAs' extraction and purification from microalgal biomass.

Unraveling metabolic alterations in Chlorella vulgaris cultivated on renewable sugars using time resolved multi-omics

The inherent metabolic versatility of Chlorella vulgaris that enables it to metabolize both inorganic and organic carbon under various trophic modes of cultivation makes it a promising candidate for industrial applications. To shed light on the metabolic flexibility of this microalga, time resolved proteomic and metabolomic studies were conducted in three distinct trophic modes (autotrophic, heterotrophic, mixotrophic) at two growth stages (end of linear growth at 6 days and during nutrient deprivation at 10 days). Sweet sorghum bagasse (SSB) hydrolysate was supplied to the cultivation medium as a renewable source of organic carbon mainly in the form of glucose. Integrated multi-omics data showed improved nitrogen assimilation, re-allocation, and recycling and increased levels of photosystem II (PS II) proteins indicating effective cellular quenching of excess electrons during mixotrophy. As external addition of organic carbon (glucose) to the cultivation medium decreases the cell's dependence on photosynthesis, an upregulation in the mitochondrial electron transport chain was recorded that led to increased cellular energy generation and hence higher growth rates under mixotrophy. Moreover, upregulation of the lipid-packaging proteins caleosin and 14_3_3 domain-containing protein resulted in maximum expression during mixotrophy suggesting a strong correlation between lipid synthesis, stabilization, and assembly. Overall, cells cultivated under mixotrophy showed better nutrient stress tolerance and redox balancing leading to higher biomass and lipid production. The study offers a panoramic view of the microalga's metabolic flexibility and contributes to a deeper understanding of the altered biochemical pathways that can be exploited to enhance algal productivity and commercial potential.

Genetic engineering of microalgae for enhanced lipid production

Microalgae have the potential to become microbial cell factories for lipid production. Their ability to convert sunlight and CO₂ into valuable lipid compounds has attracted interest from cosmetic, biofuel, food and feed industries. In order to make microalgae-derived products cost-effective and commercially competitive, enhanced growth rates and lipid productivities are needed, which require optimization of cultivation systems and strain improvement. Advances in genetic tool development and omics technologies have increased our understanding of lipid metabolism, which has opened up possibilities for targeted metabolic engineering. In this review we provide a comprehensive overview on the developments made to genetically engineer microalgal strains over the last 30 years. We focus on the strategies that lead to an increased lipid content and altered fatty acid profile. These include the genetic engineering of the fatty acid synthesis pathway, Kennedy pathway, polyunsaturated fatty acid and triacylglycerol metabolisms and fatty acid catabolism. Moreover, genetic engineering of specific transcription factors, NADPH generation and central carbon metabolism, which lead to increase of lipid accumulation are also reviewed.

Safe-Harboring based novel genetic toolkit for Nannochloropsis salina CCMP1776: Efficient overexpression of transgene via CRISPR/Cas9-Mediated Knock-in at the transcriptional hotspot

Transgene expression in microalgae can be hampered by transgene silencing and unstable expression due to position effects. To overcome this, "safe harboring" transgene expression system was established for Nannochloropsis. Initially, transformants were obtained expressing a sfGFP reporter, followed by screening for high expression of sfGFP with fluorescence-activated cell sorter (FACS). 'T1' transcriptional hotspot was identified from a mutant showing best expression of sfGFP, but did not affect growth or lipid contents. By using a Cas9 editor strain, FAD12 gene, encoding Δ12-fatty acid desaturase (FAD12), was successfully knocked-in at the T1 locus, resulting in significantly higher expression of FAD12 than those of random integration. Importantly, the "safe harbored" FAD12 transformants showed four-fold higher production of linoleic acid (LA), the product of FAD12, leading to 1.5-fold increase in eicosapentaenoic acid (EPA). This safe harboring principle provide excellent proof of the concept for successful genetic/metabolic engineering of microalgae and other organisms.

Customizing lipids from oleaginous microbes: leveraging exogenous and endogenous approaches

To meet the growing demands of the oleochemical industry, tailored lipid sources are expanding to oleaginous microbes. To control the fatty acid composition of microbial lipids, ground-breaking exogenous and endogenous approaches are being developed. Exogenous approaches employ extracellular tools such as product-specific feedstocks, process optimization, elicitors, and magnetic and mechanical energy, whereas endogenous approaches leverage biology through the use of product-specific microbes, adaptive laboratory evolution (ALE), and the creation of custom strains via random and targeted cellular engineering. We consolidate recent advances from both fields into a review that will serve as a resource for those striving to fulfill the vision of microbial cell factories for tailored lipid production.

Metal and metal(loids) removal efficiency using genetically engineered microbes: Applications and challenges

The environment is being polluted in different many with metal and metalloid pollution, mostly due to anthropogenic activity, which is directly affecting human and environmental health. Metals and metalloids are highly toxic at low concentrations and contribute primarily to the survival equilibrium of activities in the environment. However, because of non-degradable, they persist in nature and these metal and metalloids bioaccumulate in the food chain. Genetically engineered microorganisms (GEMs) mediated techniques for the removal of metals and metalloids are considered an environmentally safe and economically feasible strategy. Various forms of GEMs, including fungi, algae, and bacteria have been produced by recombinant DNA and RNA technologies, which have been used to eliminate metal and metalloids compounds from the polluted areas. Besides, GEMs have the potentiality to produce enzymes and other metabolites that are capable of tolerating metals stress and detoxify the pollutants. Thus, the aim of this review is to discuss the use of GEMs as advanced tools to produce metabolites, signaling molecules, proteins through genetic expression during metal and metalloids interaction, which help in the breakdown of persistent pollutants in the environment.

Expression of the Vitreoscilla hemoglobin gene in Nannochloropsis oceanica regulates intracellular oxygen balance under high-light

Nannochloropsis oceanica is widely used as a model photosynthetic chassis to produce fatty acids and carotenoid pigments. However, intense light typically causes excessive generation of reactive oxygen species (ROS) and photorespiration in microalgal cells, which results in decreased cell growth rate and unsaturated fatty acid content. In this study, the Vitreoscilla hemoglobin gene (vgb) was introduced into N. oceanica cells and expressed by using the light-harvesting complex promoter and its signal peptide. Compared with wild type (WT), the growth rate of transformants increased by 7.4%-18.5%, and the eicosapentaenoic acid content in an optimal transformant increased by 21.0%. Correspondingly, the intracellular ROS levels decreased by 56.9%-70.0%, and the catalase content in transformants was about 1.8 times that of WT. The photorespiration level of transformants was reduced by the measurement and calculation of the dissolved oxygen concentration under the condition of light-dark transition. The expression level of the key genes related to the photorespiration pathway in transformants was more than 80% lower than that in WT. These results indicated that Vitreoscilla hemoglobin could improve microalgal growth by reducing ROS damage and modulating photorespiration under stress conditions.

Current perspectives on integrated approaches to enhance lipid accumulation in microalgae

In recent years, research initiatives on renewable bioenergy or biofuels have been gaining momentum, not only due to fast depletion of finite reserves of fossil fuels but also because of the associated concerns for the environment and future energy security. In the last few decades, interest is growing concerning microalgae as the third-generation biofuel feedstock. The CO₂ fixation ability and conversion of it into value-added compounds, devoid of challenging food and feed crops, make these photosynthetic microorganisms an optimistic producer of biofuel from an environmental point of view. Microalgal-derived fuels are currently being considered as clean, renewable, and promising sustainable biofuel. Therefore, most research targets to obtain strains with the highest lipid productivity and a high growth rate at the lowest cultivation costs. Different methods and strategies to attain higher biomass and lipid accumulation in microalgae have been extensively reported in the previous research, but there are fewer inclusive reports that summarize the conventional methods with the modern techniques for lipid enhancement and biodiesel production from microalgae. Therefore, the current review focuses on the latest techniques and advances in different cultivation conditions, the effect of different abiotic and heavy metal stress, and the role of nanoparticles (NPs) in the stimulation of lipid accumulation in microalgae. Techniques such as genetic engineering, where particular genes associated with lipid metabolism, are modified to boost lipid synthesis within the microalgae, the contribution of "Omics" in metabolic pathway studies. Further, the contribution of CRISPR/Cas9 system technique to the production of microalgae biofuel is also briefly described.

The oleaginous astaxanthin-producing alga Chromochloris zofingiensis: potential from production to an emerging model for studying lipid metabolism and carotenogenesis

The algal lipids-based biodiesel, albeit having advantages over plant oils, still remains high in the production cost. Co-production of value-added products with lipids has the potential to add benefits and is thus believed to be a promising strategy to improve the production economics of algal biodiesel. Chromochloris zofingiensis, a unicellular green alga, has been considered as a promising feedstock for biodiesel production because of its robust growth and ability of accumulating high levels of triacylglycerol under multiple trophic conditions. This alga is also able to synthesize high-value keto-carotenoids and has been cited as a candidate producer of astaxanthin, the strongest antioxidant found in nature. The concurrent accumulation of triacylglycerol and astaxanthin enables C. zofingiensis an ideal cell factory for integrated production of the two compounds and has potential to improve algae-based production economics. Furthermore, with the advent of chromosome-level whole genome sequence and genetic tools, C. zofingiensis becomes an emerging model for studying lipid metabolism and carotenogenesis. In this review, we summarize recent progress on the production of triacylglycerol and astaxanthin by C. zofingiensis. We also update our understanding in the distinctive molecular mechanisms underlying lipid metabolism and carotenogenesis, with an emphasis on triacylglycerol and astaxanthin biosynthesis and crosstalk between the two pathways. Furthermore, strategies for trait improvements are discussed regarding triacylglycerol and astaxanthin synthesis in C. zofingiensis.

Genome engineering of Nannochloropsis with hundred-kilobase fragment deletions by Cas9 cleavages

Industrial microalgae are promising photosynthetic cell factories, yet tools for large-scale targeted genome engineering are limited. Here for the model industrial oleaginous microalga Nannochloropsis oceanica, we established a method to precisely and serially delete large genome fragments of ~100 kb from its 30.01 Mb nuclear genome. We started by identifying the 'non-essential' chromosomal regions (i.e. low expression region or LER) based on minimal gene expression under N-replete and N-depleted conditions. The largest such LER (LER1) is ~98 kb in size, located near the telomere of the 502.09-kb-long Chromosome 30 (Chr 30). We deleted 81 kb and further distal and proximal deletions of up to 110 kb (21.9% of Chr 30) in LER1 by dual targeting the boundaries with the episome-based CRISPR/Cas9 system. The telomere-deletion mutants showed normal telomeres consisting of CCCTAA repeats, revealing telomere regeneration capability after losing the distal part of Chr 30. Interestingly, the deletions caused no significant alteration in growth, lipid production or photosynthesis (transcript-abundance change for < 3% genes under N depletion). We also achieved double-deletion of both LER1 and LER2 (from Chr 9) that total ~214 kb at maximum, which can result in slightly higher growth rate and biomass productivity than the wild-type. Therefore, loss of the large, yet 'non-essential' regions does not necessarily sacrifice important traits. Such serial targeted deletions of large genomic regions had not been previously reported in microalgae, and will accelerate crafting minimal genomes as chassis for photosynthetic production.

Overexpression of the Transcription Factor AtLEC1 Significantly Improved the Lipid Content of Chlorella ellipsoidea

Microalgae are considered to be a highly promising source for the production of biodiesel. However, the regulatory mechanism governing lipid biosynthesis has not been fully elucidated to date, and the improvement of lipid accumulation in microalgae is essential for the effective production of biodiesel. In this study, LEAFY COTYLEDON1 (LEC1) from Arabidopsis thaliana, a transcription factor (TF) that affects lipid content, was transferred into Chlorella ellipsoidea. Compared with wild-type (WT) strains, the total fatty acid content and total lipid content of AtLEC1 transgenic strains were significantly increased by 24.20–32.65 and 22.14–29.91%, respectively, under mixotrophic culture conditions and increased by 24.4–28.87 and 21.69–30.45%, respectively, under autotrophic conditions, while the protein content of the transgenic strains was significantly decreased by 18.23–21.44 and 12.28–18.66%, respectively, under mixotrophic and autotrophic conditions. Fortunately, the lipid and protein content variation did not affect the growth rate and biomass of transgenic strains under the two culture conditions. According to the transcriptomic data, the expression of 924 genes was significantly changed in the transgenic strain (LEC1-1). Of the 924 genes, 360 were upregulated, and 564 were downregulated. Based on qRT-PCR results, the expression profiles of key genes in the lipid synthesis pathway, such as ACCase, GPDH, PDAT1, and DGAT1, were significantly changed. By comparing the differentially expressed genes (DEGs) regulated by AtLEC1 in C. ellipsoidea and Arabidopsis, we observed that approximately 59% (95/160) of the genes related to lipid metabolism were upregulated in AtLEC1 transgenic Chlorella. Our research provides a means of increasing lipid content by introducing exogenous TF and presents a possible mechanism of AtLEC1 regulation of lipid accumulation in C. ellipsoidea.

Biological approaches practised using genetically engineered microbes for a sustainable environment: A review

Conventional methods used to remediate toxic substances from the environment have failed drastically, and thereby, advancement in newer remediation techniques can be one of the ways to improve the quality of bioremediation. The increased environmental pollution led to the exploration of microorganisms and construction of genetically engineered microbes (GEMs) for pollution abatement through bioremediation. The present review deals with the successful bioremediation techniques and approaches practised using genetically modified or engineered microbes. In the present scenario, physical and chemical strategies have been practised for the remediation of domestic and industrial wastes but these techniques are expensive and toxic to the environment. Involving engineered microbes can provide a much safer and cost effective strategy in comparison with the other techniques. With the aid of biotechnology and genetic engineering, GEMs are designed by transforming microbes with a more potent protein to overexpress the desired character. GEMs such as bacteria, fungi and algae have been used to degrade oil spills, camphor, hexane, naphthalene, toluene, octane, xylene, halobenzoates, trichloroethylene etc. These engineered microbes are more potent than the natural strains and have higher degradative capacities with quick adaptation for various pollutants as substrates or cometabolize. The road ahead for the implementation of genetic engineering to produce such organisms for the welfare of the environment and finally, public health is indeed long and worthwhile.

AP2/ERF and R2R3-MYB family transcription factors: potential associations between temperature stress and lipid metabolism in Auxenochlorella protothecoides

BACKGROUND

Both APETALA2/Ethylene Responsive Factor (AP2/ERF) superfamily and R2R3-MYB family were from one of the largest diverse families of transcription factors (TFs) in plants, and played important roles in plant development and responses to various stresses. However, no systematic analysis of these TFs had been conducted in the green algae A. protothecoides heretofore. Temperature was a critical factor affecting growth and lipid metabolism of A. protothecoides. It also remained largely unknown whether these TFs would respond to temperature stress and be involved in controlling lipid metabolism process.

RESULTS

Hereby, a total of six AP2 TFs, six ERF TFs and six R2R3-MYB TFs were identified and their expression profiles were also analyzed under low-temperature (LT) and high-temperature (HT) stresses. Meanwhile, differential adjustments of lipid pathways were triggered, with enhanced triacylglycerol accumulation. A co-expression network was built between these 18 TFs and 32 lipid-metabolism-related genes, suggesting intrinsic associations between TFs and the regulatory mechanism of lipid metabolism.

CONCLUSIONS

This study represented an important first step towards identifying functions and roles of AP2 superfamily and R2R3-MYB family in lipid adjustments and response to temperature stress. These findings would facilitate the biotechnological development in microalgae-based biofuel production and the better understanding of photosynthetic organisms' adaptive mechanism to temperature stress.

The NanDeSyn database for Nannochloropsis systems and synthetic biology

Nannochloropsis species, unicellular industrial oleaginous microalgae, are model organisms for microalgal systems and synthetic biology. To facilitate community-based annotation and mining of the rapidly accumulating functional genomics resources, we have initiated an international consortium and present a comprehensive multi-omics resource database named Nannochloropsis Design and Synthesis (NanDeSyn; http://nandesyn.single-cell.cn). Via the Tripal toolkit, it features user-friendly interfaces hosting genomic resources with gene annotations and transcriptomic and proteomic data for six Nannochloropsis species, including two updated genomes of Nannochloropsis oceanica IMET1 and Nannochloropsis salina CCMP1776. Toolboxes for search, Blast, synteny view, enrichment analysis, metabolic pathway analysis, a genome browser, etc. are also included. In addition, functional validation of genes is indicated based on phenotypes of mutants and relevant bibliography. Furthermore, epigenomic resources are also incorporated, especially for sequencing of small RNAs including microRNAs and circular RNAs. Such comprehensive and integrated landscapes of Nannochloropsis genomics and epigenomics will promote and accelerate community efforts in systems and synthetic biology of these industrially important microalgae.

Sustainable environmental management and related biofuel technologies

Environmental sustainability criteria and rising energy demands, exhaustion of conventional resources of energy followed by environmental degradation due to abrupt climate changes have shifted the attention of scientists to seek renewable sources of green and clean energy for sustainable development. Bioenergy is an excellent alternative since it can be applied for several energy-requirements after utilizing suitable conversion methodology. This review elucidates all aspects of biofuels (bioethanol, biodiesel, and butanol) and their sustainability criteria. The principal focus is on the latest developments in biofuel production chiefly stressing on the role of nanotechnology. A plethora of investigations regarding the emerging techniques for process improvement like integration methods, less energy-intensive distillation techniques, and bioengineering of microorganisms are discussed. This can assist in making biofuel-production in a real-world market more economically and environmentally viable.

Enhancement of Lipid Production under Heterotrophic Conditions by Overexpression of an Endogenous bZIP Transcription Factor in Chlorella sp. HS2

Transcription factor engineering to regulate multiple genes has shown promise in the field of microalgae genetic engineering. Here, we report the first use of transcription factor engineering in Chlorella sp. HS2, thought to have potential for producing biofuels and bioproducts. We identified seven endogenous bZIP transcription factors in Chlorella sp. HS2 and named them HSbZIP1 through HSbZIP7. We overexpressed HSbZIP1, a C-type bZIP transcription factor, in Chlorella sp. HS2 with the goal of enhancing lipid production. Phenotype screening under heterotrophic conditions showed that all transformants exhibited increased fatty acid production. In particular, HSbZIP1 37 and 58 showed fatty acid methyl ester (FAME) yields of 859 and 1,052 mg/l, respectively, at day 10 of growth under heterotrophic conditions, and these yields were 74% and 113% higher, respectively, than that of WT. To elucidate the mechanism underlying the improved phenotypes, we identified candidate HSbZIP1-regulated genes via transcription factor binding site analysis. We then selected three genes involved in fatty acid synthesis and investigated mRNA expression levels of the genes by qRTPCR. The result revealed that the possible HSbZIP1-regulated genes involved in fatty acid synthesis were upregulated in the HSbZIP1 transformants. Taken together, our results demonstrate that HSbZIP1 can be utilized to improve lipid production in Chlorella sp. HS2 under heterotrophic conditions.

Advances in AP2/ERF super-family transcription factors in plant

In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.

Genetic engineering of microalgae for enhanced biorefinery capabilities

Microalgae-based bioproducts are in limelight because of their promising future, novel characteristics, the current situation of population needs, and rising prices of rapidly depleting energy resources. Algae-based products are considered as clean sustainable energy and food resources. At present, they are not commercialized due to their high production cost and low yield. In recent years, novel genome editing tools like RNAi, ZNFs, TALENs, and CRISPR/Cas9 are used to enhance the quality and quantity of the desired products. Genetic and metabolic engineering are frequently applied because of their rapid and precise results than random mutagenesis. Omic approaches help enhance biorefinery capabilities and are now in the developing stage for algae. The future is very bright for transgenic algae with increased biomass yield, carbon dioxide uptake rate, accumulating high-value compounds, reduction in cultivation, and production costs, thus reaching the goal in the global algal market and capital flow. However, microalgae are primary producers and any harmful exposure to the wild strains can affect the entire ecosystem. Therefore, strict regulation and monitoring are required to assess the potential risks before introducing genetically modified microalgae into the natural ecosystem.

Synechocystis sp. PCC 6803 overexpressing genes involved in CBB cycle and free fatty acid cycling enhances the significant levels of intracellular lipids and secreted free fatty acids

The integrative aspect on carbon fixation and lipid production is firstly implemented in cyanobacterium Synechocystis sp. PCC 6803 using metabolic engineering approach. Genes related to Calvin–Benson–Bassham (CBB) cycle including rbcLXS and glpD and free fatty acid recycling including aas encoding acyl-ACP synthetase were practically manipulated in single, double and triple overexpressions via single homologous recombination. The significantly increased growth rate and intracellular pigment contents were evident in glpD-overexpressing (OG) strain among all strains studied under normal growth condition. The triple aas_glpD_rbcLXS-overexpressing (OAGR) strain notably gave the highest contents of both intracellular lipids and extracellular free fatty acids (FFAs) of about 35.9 and 9.6% w/DCW, respectively, when compared to other strains at day 5 of cultivation. However, the highest intracellular lipid titer and production rate were observed in OA strain at day 5 (228.7 mg/L and 45.7 mg/L/day, respectively) and OG strain at day 10 (358.3 mg/L and 35.8 mg/L/day, respectively) due to their higher growth. For fatty acid (FA) compositions, the main saturated fatty acid of palmitic acid (C16:0) was dominantly found in both intracellular lipid and secreted FFAs fractions. Notably, intracellular FA proportion of myristic acid (C14:0) was induced in all engineered strains whereas the increase of stearic acid (C18:0) composition was found in extracellular FFAs fraction. Altogether, these overexpressing strains efficiently produced higher lipid production via homeostasis balance on both its lipid synthesis and FFAs secretion.

Development and characterization of a Nannochloropsis mutant with simultaneously enhanced growth and lipid production

BACKGROUND

The necessity to develop high lipid-producing microalgae is emphasized for the commercialization of microalgal biomass, which is environmentally friendly and sustainable. Nannochloropsis are one of the best industrial microalgae and have been widely studied for their lipids, including high-value polyunsaturated fatty acids (PUFAs). Many reports on the genetic and biological engineering of Nannochloropsis to improve their growth and lipid contents have been published.

RESULTS

We performed insertional mutagenesis in Nannochloropsis salina, and screened mutants with high lipid contents using fluorescence-activated cell sorting (FACS). We isolated a mutant, Mut68, which showed improved growth and a concomitant increase in lipid contents. Mut68 exhibited 53% faster growth rate and 34% higher fatty acid methyl ester (FAME) contents after incubation for 8 days, resulting in a 75% increase in FAME productivity compared to that in the wild type (WT). By sequencing the whole genome, we identified the disrupted gene in Mut68 that encoded trehalose-6-phosphate (T6P) synthase (TPS). TPS is composed of two domains: TPS domain and T6P phosphatase (TPP) domain, which catalyze the initial formation of T6P and dephosphorylation to trehalose, respectively. Mut68 was disrupted at the TPP domain in the C-terminal half, which was confirmed by metabolic analyses revealing a great reduction in the trehalose content in Mut68. Consistent with the unaffected N-terminal TPS domain, Mut68 showed moderate increase in T6P that is known for regulation of sugar metabolism, growth, and lipid biosynthesis. Interestingly, the metabolic analyses also revealed a significant increase in stress-related amino acids, including proline and glutamine, which may further contribute to the Mut68 phenotypes.

CONCLUSION

We have successfully isolated an insertional mutant showing improved growth and lipid production. Moreover, we identified the disrupted gene encoding TPS. Consistent with the disrupted TPP domain, metabolic analyses revealed a moderate increase in T6P and greatly reduced trehalose. Herein, we provide an excellent proof of concept that the selection of insertional mutations via FACS can be employed for the isolation of mutants with improved growth and lipid production. In addition, trehalose and genes encoding TPS will provide novel targets for chemical and genetic engineering, in other microalgae and organisms as well as Nannochloropsis.

Potential and Challenges of Improving Photosynthesis in Algae

Sunlight energy largely exceeds the energy required by anthropic activities, and therefore its exploitation represents a major target in the field of renewable energies. The interest in the mass cultivation of green microalgae has grown in the last decades, as algal biomass could be employed to cover a significant portion of global energy demand. Advantages of microalgal vs. plant biomass production include higher light-use efficiency, efficient carbon capture and the valorization of marginal lands and wastewaters. Realization of this potential requires a decrease of the current production costs, which can be obtained by increasing the productivity of the most common industrial strains, by the identification of factors limiting biomass yield, and by removing bottlenecks, namely through domestication strategies aimed to fill the gap between the theoretical and real productivity of algal cultures. In particular, the light-to-biomass conversion efficiency represents one of the major constraints for achieving a significant improvement of algal cell lines. This review outlines the molecular events of photosynthesis, which regulate the conversion of light into biomass, and discusses how these can be targeted to enhance productivity through mutagenesis, strain selection or genetic engineering. This review highlights the most recent results in the manipulation of the fundamental mechanisms of algal photosynthesis, which revealed that a significant yield enhancement is feasible. Moreover, metabolic engineering of microalgae, focused upon the development of renewable fuel biorefineries, has also drawn attention and resulted in efforts for enhancing productivity of oil or isoprenoids.

Expression of galactinol synthase from Ammopiptanthus nanus in tomato improves tolerance to cold stress

Soluble carbohydrates not only directly affect plant growth and development but also act as signal molecules in processes that enhance tolerance to cold stress. Raffinose family oligosaccharides (RFOs) are an example and play an important role in abiotic stress tolerance. This study aimed to determine whether galactinol, a key limiting factor in RFO biosynthesis, functions as a signal molecule in triggering cold tolerance. Exposure to low temperatures induces the expression of galactinol synthase (AnGolS1) in Ammopiptanthus nanus, a desert plant that survives temperatures between -30 °C to 47 °C. AnGolS1 has a greater catalytic activity than tomato galactinol synthase (SlGolS2). Moreover, SlGolS2 is expressed only at low levels. Expression of AnGolS1 in tomato enhanced cold tolerance and led to changes in the sugar composition of the seeds and seedlings. AnGolS1 transgenic tomato lines exhibited an enhanced capacity for ethylene (ET) signaling. The application of galactinol abolished the repression of the ET signaling pathway by 1-methylcyclopropene during seed germination. In addition, the expression of ERF transcription factors was increased. Galactinol may therefore act as a signal molecule affecting the ET pathway.

Improving lipid production by strain development in microalgae: Strategies, challenges and perspectives

Over the past decade, the number of original articles and reviews presenting microalgae as a promising feedstock for biodiesel has increased tremendously. Many improvements of microalgae have been achieved through selection and strain development for industrial applications. However, the large-scale production of lipids for commercialization is not yet realistic because the production is still much more expensive than that of agricultural products. This review summarizes recent research on the induction of lipid biosynthesis in microalgae and the various strategies of genetic and metabolic engineering for enhancing lipid production. Strain engineering targets are proposed based on these strategies. To address current limitations of strain engineering for lipid production, this review provides insights on recent engineering strategies based on molecular tools and methods, and also discusses further perspectives.

Transgenic microalgae as bioreactors

Microalgae are unicellular organisms that act as the crucial primary producers all over the world, typically found in marine and freshwater environments. Most of them can live photo-autotrophically, reproduce rapidly, and accumulate biomass in a short period efficiently. To adapt to the uninterrupted change of the environment, they evolve and differentiate continuously. As a result, some of them evolve special abilities such as toleration of extreme environment, generation of sophisticated structure to adapt to the environment, and avoid predators. Microalgae are believed to be promising bioreactors because of their high lipid and pigment contents. Genetic engineering technologies have given revolutions in the microalgal industry, which decoded the secrets of microalgal genes, express recombinant genes in microalgal genomes, and largely soar the accumulation of interested components in transgenic microalgae. However, owing to several obstructions, the industry of transgenic microalgae is still immature. Here, we provide an overview to emphasize the advantage and imperfection of the existing transgenic microalgal bioreactors.

Biomass and lipid induction strategies in microalgae for biofuel production and other applications

The use of fossil fuels has been strongly related to critical problems currently affecting society, such as: global warming, global greenhouse effects and pollution. These problems have affected the homeostasis of living organisms worldwide at an alarming rate. Due to this, it is imperative to look for alternatives to the use of fossil fuels and one of the relevant substitutes are biofuels. There are different types of biofuels (categories and generations) that have been previously explored, but recently, the use of microalgae has been strongly considered for the production of biofuels since they present a series of advantages over other biofuel production sources: (a) they don’t need arable land to grow and therefore do not compete with food crops (like biofuels produced from corn, sugar cane and other plants) and; (b) they exhibit rapid biomass production containing high oil contents, at least 15 to 20 times higher than land based oleaginous crops. Hence, these unicellular photosynthetic microorganisms have received great attention from researches to use them in the large-scale production of biofuels. However, one disadvantage of using microalgae is the high economic cost due to the low-yields of lipid content in the microalgae biomass. Thus, development of different methods to enhance microalgae biomass, as well as lipid content in the microalgae cells, would lead to the development of a sustainable low-cost process to produce biofuels. Within the last 10 years, many studies have reported different methods and strategies to induce lipid production to obtain higher lipid accumulation in the biomass of microalgae cells; however, there is not a comprehensive review in the literature that highlights, compares and discusses these strategies. Here, we review these strategies which include modulating light intensity in cultures, controlling and varying CO₂ levels and temperature, inducing nutrient starvation in the culture, the implementation of stress by incorporating heavy metal or inducing a high salinity condition, and the use of metabolic and genetic engineering techniques coupled with nanotechnology.

Glucose-6-Phosphate Dehydrogenase from the Oleaginous Microalga Nannochloropsis Uncovers Its Potential Role in Promoting Lipogenesis

Microalgae have long been considered as potential biological feedstock for the production of wide array of bioproducts, such as biofuel feedstock because of their lipid accumulating capability. However, lipid productivity of microalgae is still far below commercial viability. Here, a glucose-6-phosphate dehydrogenase from the oleaginous microalga Nannochloropsis oceanica is identified and heterologously expressed in the green microalga Chlorella pyrenoidosa to characterize its function in the pentose phosphate pathway. It is found that the G6PD enzyme activity toward NADPH production is increased by 2.19-fold in engineered microalgal strains. Lipidomic analysis reveals up to 3.09-fold increase of neutral lipid content in the engineered strains, and lipid yield is gradually increased throughout the cultivation phase and saturated at the stationary phase. Moreover, cellular physiological characteristics including photosynthesis and growth rate are not impaired. Collectively, these results reveal the pivotal role of glucose-6-phosphate dehydrogenase from N. oceanica in NADPH supply, demonstrating that provision of reducing power is crucial for microalgal lipogenesis and can be a potential target for metabolic engineering.

Expression of the Arabidopsis WRINKLED 1 transcription factor leads to higher accumulation of palmitate in soybean seed

Soybean (Glycine max [L.] Merr.) is a commodity crop highly valued for its protein and oil content. The high percentage of polyunsaturated fatty acids in soybean oil results in low oxidative stability, which is a key parameter for usage in baking, high temperature frying applications, and affects shelf life of packaged products containing soybean oil. Introduction of a seed-specific expression cassette carrying the Arabidopsis transcription factor WRINKLED1 (AtWRI1) into soybean, led to seed oil with levels of palmitate up to approximately 20%. Stacking of the AtWRI1 transgenic allele with a transgenic locus harbouring the mangosteen steroyl-ACP thioesterase (GmFatA) resulted in oil with total saturates up to 30%. The creation of a triple stack in soybean, wherein the AtWRI1 and GmFatA alleles were combined with a FAD2-1 silencing allele led to the synthesis of an oil with 28% saturates and approximately 60% oleate. Constructs were then assembled that carry a dual FAD2-1 silencing element/GmFatA expression cassette, alone or combined with an AtWRI1 cassette. These plasmids are designated pPTN1289 and pPTN1301, respectively. Transgenic events carrying the T-DNA of pPTN1289 displayed an oil with stearate levels between 18% and 25%, and oleate in the upper 60%, with reduced palmitate (<5%). While soybean events harboring transgenic alleles of pPTN1301 had similar levels of stearic and oleate levels as that of the pPTRN1289 events, but with levels of palmitate closer to wild type. The modified fatty acid composition results in an oil with higher oxidative stability, and functionality attributes for end use in baking applications.

Multiomics analysis reveals a distinct mechanism of oleaginousness in the emerging model alga Chromochloris zofingiensis

Chromochloris zofingiensis, featured due to its capability to simultaneously synthesize triacylglycerol (TAG) and astaxanthin, is emerging as a leading candidate alga for production uses. To better understand the oleaginous mechanism of this alga, we conducted a multiomics analysis by systematically integrating time-resolved transcriptomes, lipidomes and metabolomes in response to nitrogen deprivation. The data analysis unraveled the distinct mechanism of TAG accumulation, which involved coordinated stimulation of multiple biological processes including supply of energy and reductants, carbon reallocation from protein and starch, and 'pushing' and 'pulling' carbon to TAG synthesis. Unlike the model alga Chlamydomonas, de novo fatty acid synthesis in C. zofingiensis was promoted, together with enhanced turnover of both glycolipids and phospholipids, supporting the drastic need of acyls for TAG assembly. Moreover, genomewide analysis identified many key functional enzymes and transcription factors that had engineering potential for TAG modulation. Two genes encoding glycerol-3-phosphate acyltransferase (GPAT), the first committed enzyme for TAG assembly, were found in the C. zofingiensis genome; in vivo functional characterization revealed that extrachloroplastic GPAT instead of chloroplastic GPAT played a central role in TAG synthesis. These findings illuminate distinct oleaginousness mechanisms in C. zofingiensis and pave the way towards rational manipulation of this alga to becone an emerging model for trait improvements.

Metabolic Engineering Strategies for the Enhanced Microalgal Production of Long-Chain Polyunsaturated Fatty Acids (LC-PUFAs)

Long-chain polyunsaturated fatty acids (LC-PUFAs), largely obtained from fish oil, serve as valuable dietary supplements with many health benefits, especially arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid. In recent years, interest in the sustainable production of LC-PUFAs using heterologous production hosts has drastically increased because overfishing and polluted oceans have led to a gradual decline in the supply of LC-PUFAs from fish oil in the last few decades. Some species of microalgae have been considered to be an ideal producer of LC-PUFAs as they inherently accumulate large amounts of LC-PUFAs and utilize CO₂ using light energy. Also, a growing number of genetic toolboxes have become available, and the microalgal cultivation process is amenable to a scale-up. In fact, tremendous progress has been achieved in the development of high-performance strains of microalgae through metabolic engineering that has led to the efficient production of fatty acids and various derivatives in the last decade. This review discusses metabolic engineering strategies that have contributed to the enhanced production of LC-PUFAs using microalgae, including optimizing fatty acid biosynthetic pathway and intracellular supply of precursors and cofactors, as well as engineering transcription factors.

WRINKLED1 Is Subject to Evolutionary Conserved Negative Autoregulation

High accumulation of storage compounds such as oil and starch are economically important traits of most agricultural crops. The genetic network determining storage compounds composition in crops has been the target of many biotechnological endeavors. Especially WRINKLED1 (WRI1), a well-known key transcription factor involved in the allocation of carbon into oil, has attracted much interest. Here we investigate the presence of an autoregulatory system involving WRI1 through transient expression in Nicotiana benthamiana leaves. Different lengths of the Arabidopsis WRI1 promotor region were coupled to a GUS reporter gene and the activity was measured when combined with constitutive expression of different WRI1 homologs from Arabidopsis thaliana, oat (Avena sativa L.), yellow nutsedge (Cyperus esculentus L.), and potato (Solanum tuberosum L.). We could show that increasing levels of each WRI1 homolog reduced the transcriptional activity of the Arabidopsis WRI1 upstream region. Through structural analysis and domain swapping between oat and Arabidopsis WRI1, we were able to determine that the negative autoregulation was clearly dependent on the DNA-binding AP2-domains. A DNA/protein interaction assay showed that AtWRI1 is unable to bind to its corresponding upstream region indicating non-direct interaction in vivo. Taken together, our results demonstrate a negative feedback loop of WRI1 expression and that it is an indirect interaction most likely caused by downstream targets of WRI1. We also show that it is possible to release WRI1 expression from this autoregulation by creating semi-synthetic WRI1 homologs increasing the potential use of WRI1 in biotechnological applications.

The lipid biochemistry of eukaryotic algae

Algal lipid metabolism fascinates both scientists and entrepreneurs due to the large diversity of fatty acyl structures that algae produce. Algae have therefore long been studied as sources of genes for novel fatty acids; and, due to their superior biomass productivity, algae are also considered a potential feedstock for biofuels. However, a major issue in a commercially viable "algal oil-to-biofuel" industry is the high production cost, because most algal species only produce large amounts of oils after being exposed to stress conditions. Recent studies have therefore focused on the identification of factors involved in TAG metabolism, on the subcellular organization of lipid pathways, and on interactions between organelles. This has been accompanied by the development of genetic/genomic and synthetic biological tools not only for the reference green alga Chlamydomonas reinhardtii but also for Nannochloropsis spp. and Phaeodactylum tricornutum. Advances in our understanding of enzymes and regulatory proteins of acyl lipid biosynthesis and turnover are described herein with a focus on carbon and energetic aspects. We also summarize how changes in environmental factors can impact lipid metabolism and describe present and potential industrial uses of algal lipids.

Increased biomass and lipid production by continuous cultivation of Nannochloropsis salina transformant overexpressing a bHLH transcription factor

Microalgae are promising feedstocks for sustainable and eco-friendly production of biomaterials, which can be improved by genetic engineering. It is also necessary to optimize the processes to produce biomaterials from engineered microalgae. We previously reported that genetic improvements of an industrial microalga Nannochloropsis salina by overexpressing a basic helix-loop-helix transcription factor (NsbHLH2). These transformants showed an improved growth and lipid production particularly during the early phase of culture under batch culture. However, they had faster uptake of nutrients, resulting in earlier starvation and reduced growth during the later stages. We attempted to optimize the growth and lipid production by growing one of the transformants in continuous culture with variable dilution rate and feed nitrogen concentration. Relative to wild-type, NsbHLH2 transformant consumed more nitrate at a high dilution rate (0.5 day ^-1 ), and had greater biomass production. Subsequently, nitrogen limitation at continuous cultivation led to an increased fatty acid methyl ester production by 83.6 mg l ^-1 day ^-1 . To elucidate genetic mechanisms, we identified the genes containing E-boxes, known as binding sites for bHLH transcription factors. Among these, we selected 18 genes involved in the growth and lipid metabolism, and revealed their positive contribution to the phenotypes via quantitative real-time polymerase chain reaction. These results provide proof-of-concept that NsbHLH2 can be used to produce biomass and lipids.

Characterization of type I and type II diacylglycerol acyltransferases from the emerging model alga Chlorella zofingiensis reveals their functional complementarity and engineering potential

BACKGROUND

The green alga Chlorella zofingiensis has been recognized as an industrially relevant strain because of its robust growth under multiple trophic conditions and the potential for simultaneous production of triacylglycerol (TAG) and the high-value keto-carotenoid astaxanthin. Nevertheless, the mechanism of TAG synthesis remains poorly understood in C. zofingiensis. Diacylglycerol acyltransferase (DGAT) is thought to catalyze the committed step of TAG assembly in the Kennedy pathway. C. zofingiensis genome is predicted to possess eleven putative DGAT-encoding genes, the greatest number ever found in green algae, pointing to the complexity of TAG assembly in the alga.

RESULTS

The transcription start site of C. zofingiensis DGATs was determined by 5'-rapid amplification of cDNA ends (RACE), and their coding sequences were cloned and verified by sequencing, which identified ten DGAT genes (two type I DGATs designated as CzDGAT1A and CzDGAT1B, and eight type II DGATs designated as CzDGTT1 through CzDGTT8) and revealed that the previous gene models of seven DGATs were incorrect. Function complementation in the TAG-deficient yeast strain confirmed the functionality of most DGATs, with CzDGAT1A and CzDGTT5 having the highest activity. In vitro DGAT assay revealed that CzDGAT1A and CzDGTT5 preferred eukaryotic and prokaryotic diacylglycerols (DAGs), respectively, and had overlapping yet distinctive substrate specificity for acyl-CoAs. Subcellular co-localization experiment in tobacco leaves indicated that both CzDGAT1A and CzDGTT5 were localized at endoplasmic reticulum (ER). Upon nitrogen deprivation, TAG was drastically induced in C. zofingiensis, accompanied by a considerable up-regulation of CzDGAT1A and CzDGTT5. These two genes were probably regulated by the transcription factors (TFs) bZIP3 and MYB1, as suggested by the yeast one-hybrid assay and expression correlation. Moreover, heterologous expression of CzDGAT1A and CzDGTT5 promoted TAG accumulation and TAG yield in different hosts including yeast and oleaginous alga.

CONCLUSIONS

Our study represents a pioneering work on the characterization of both type I and type II C. zofingiensis DGATs by systematically integrating functional complementation, in vitro enzymatic assay, subcellular localization, yeast one-hybrid assay and overexpression in yeast and oleaginous alga. These results (1) update the gene models of C. zofingiensis DGATs, (2) shed light on the mechanism of oleaginousness in which CzDGAT1A and CzDGTT5, have functional complementarity and probably work in collaboration at ER contributing to the abundance and complexity of TAG, and (3) provide engineering targets for future trait improvement via rational manipulation of this alga as well as other industrially relevant ones.